Variant report

Variant	rs758167
Chromosome Location	chr12:1915559-1915560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1912567..1917043-chr12:1917472..1921043,5	K562	blood:
2	chr12:1905522..1910417-chr12:1912711..1915784,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRTM2-5	chr12:1915457-1915724	NONHSAT025425
2	lnc-LRTM2-5	chr12:1915457-1915724	NONHSAT025426

Variant related genes	Relation type
ENSG00000151062	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12823985	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16928759	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34708777	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34715276	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35000021	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59962311	0.80[AMR][1000 genomes]
rs7316101	0.80[AMR][1000 genomes]
rs7960114	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs970482	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv430442	chr12:1889823-1982151	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv556996	chr12:1891372-1934920	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv1824001	chr12:1896738-1951940	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv898592	chr12:1901485-1937801	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv898593	chr12:1901485-1962759	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv468965	chr12:1907853-1931396	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv556997	chr12:1907853-1931396	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv468966	chr12:1907853-1933553	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv556998	chr12:1907853-1933553	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv470259	chr12:1907853-1945042	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv518013	chr12:1914273-1952990	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs758167	MAP4K4	trans	brain	seeQTL
rs758167	PKP4	trans	brain	seeQTL
rs758167	KIF1C	trans	brain	seeQTL
rs758167	MBP	trans	brain	seeQTL
rs758167	KIF5B	trans	brain	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1905600-1928600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:1910000-1916400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:1910000-1916400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:1910800-1920000	Weak transcription	Primary B cells from cord blood	blood
5	chr12:1911600-1919200	Weak transcription	Osteobl	bone
6	chr12:1912800-1917000	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr12:1913200-1916200	Enhancers	Left Ventricle	heart
8	chr12:1913400-1917000	Enhancers	Duodenum Mucosa	Duodenum
9	chr12:1913800-1916200	Enhancers	Fetal Muscle Trunk	muscle
10	chr12:1913800-1916400	Enhancers	Right Ventricle	heart
11	chr12:1913800-1916800	Enhancers	Fetal Muscle Leg	muscle
12	chr12:1913800-1917000	Enhancers	Fetal Intestine Large	intestine
13	chr12:1913800-1917600	Enhancers	Placenta	Placenta
14	chr12:1913800-1918800	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr12:1913800-1920000	Enhancers	Fetal Thymus	thymus
16	chr12:1913800-1920400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr12:1914000-1916000	Enhancers	Adipose Nuclei	Adipose
18	chr12:1914000-1916000	Enhancers	Fetal Heart	heart
19	chr12:1914000-1917600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:1914000-1917600	Enhancers	Fetal Intestine Small	intestine
21	chr12:1914000-1920400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:1914200-1915600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr12:1914200-1915600	Enhancers	Psoas Muscle	Psoas
24	chr12:1914200-1918400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr12:1914200-1918600	Weak transcription	K562	blood
26	chr12:1914200-1919600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:1914200-1919800	Weak transcription	Primary T cells from cord blood	blood
28	chr12:1914200-1920000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:1914200-1920600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:1914400-1915600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:1914400-1915600	Weak transcription	Fetal Brain Male	brain
32	chr12:1914400-1916400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:1914400-1916800	Weak transcription	GM12878-XiMat	blood
34	chr12:1914400-1917400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:1914400-1918800	Weak transcription	Brain Germinal Matrix	brain
36	chr12:1914400-1919800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:1914400-1919800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr12:1914400-1920400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:1914600-1917800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:1914800-1916000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:1914800-1916200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr12:1915000-1915600	Enhancers	Fetal Lung	lung
43	chr12:1915000-1915800	Enhancers	Stomach Mucosa	stomach
44	chr12:1915000-1916200	Enhancers	HSMMtube	muscle
45	chr12:1915200-1915600	Genic enhancers	HepG2	liver
46	chr12:1915200-1916000	Enhancers	NHDF-Ad	bronchial
47	chr12:1915200-1916200	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr12:1915200-1917800	Weak transcription	Spleen	Spleen
49	chr12:1915200-1919600	Weak transcription	Lung	lung
50	chr12:1915400-1915800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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